user guide update

docs/manual/docs/user-guide/analyzing/data.md

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+# Analyze and visualize data {#analyzing_data}
+
+## Data accessible using download services (WFS)
+
+All datasets described in metadata records and accessible through a download services (ie WFS) can be analyzed to improve search and data visualization. The catalog collect WFS features and index them.
+
+![](img/mechanism.png)
+
+Elasticsearch needs to be installed and configured (See [installing-index](installing-index.md)).
+
+Once collected, filtering is available in the map viewer for this layer. The filter interface provides faceting and export capabilities. The map viewer tries to connect to a WFS service by substituting WMS by WFS in the service URL. If a WFS service is responding with a feature type having the same name as the WMS, the filter panel provides the option to index the features. User needs to be identified to run the indexing task.
+
+![](img/layernotindexed.png)
+
+Once indexed, all users can access the filtering menu providing:
+
+-   a full text search on all fields
+-   a control to display or not the heatmap
+-   facets on all fields (computing automatically range facet for numbers)
+-   table action display all values
+-   filter action apply the filters to the WMS layers using SLD
+
+![](img/filtering.png)
+
+Click on the table menu to display the attributes. Double click a row in the table to zoom to a feature.
+
+![](img/tableview.png)
+
+Spatial filters can also be applied.
+
+![](img/filteringlayer.png)
+
+## Feature type customization
+
+By default, the filter panel is generated from Elasticsearch index. But you customise it for a specific WFS Feature Type.
+
+The customisation is done by a JSON config inserted in the gmd:applicationProfile section of the online resource in the metadata.
+
+Here the options:
+
+    {
+    "fields": [{
+      "name": "PNT_PROF",
+      // non disponible actuellement
+      "type": "double",
+      "fq" : {
+        "facet.interval": "PNT_PROF_d",
+        "facet.interval.set": ["[0,10]", "(10,10000]"],
+       or
+        "facet.range": "PNT_PROF_d",
+        "facet.range.start": "0",
+        "facet.range.end": "10000",
+        "facet.range.gap": "300"
+       or
+        "facet.range": "PNT_PROF_d",
+        "facet.range.classes": "5" // Get min, max and compute gap on 5 classes
+      }
+    }, {
+      "name": "GRIDCODE"
+    }, {
+      "name": "LABEL",
+      "label" : {"fr": "monLabel", "en": "myLabel"}
+    }],
+    "tokenize": {"GRIDCODE": ",", "PARCELLE": "/"},
+    "heatmap": true
+    }
+
+You can
+
+-   restrict the fields used for filter
+-   specify your own ranges for numeric values
+-   set your label
+-   manage tokenized fields
+-   enable heatmap

docs/manual/docs/user-guide/analyzing/index.md

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+# Analyzing data {#analyzing}
+
+-   [Metadata](metadata.md)
+-   [Data](data.md)

docs/manual/docs/user-guide/analyzing/metadata.md

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+# Statistics on catalog content {#analyzing_metadata}
+
+The administration panel provides statistics on search and on records in the catalog.

docs/manual/docs/user-guide/associating-resources/cite.md

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+# Cite a resource {#cite}
+
+The catalogue can provide an automatic citation based on information provided in the metadata record.
+
+![](img/citation.png)
+
+The citation can be use to cite a dataset in publications.
+
+## Citation text
+
+The citation generated by default follows general conventions on how to cite a dataset but can be customized.
+
+The default is: * list of authors (and organisation) * publication year * title * list of publisher * DOI URL or landing page URL.
+
+These are the data needed to create DOI (see [doi](doi.md)).
+
+Customization of the citation can be done in `schemas/iso19115-3.2018/src/main/plugin/iso19115-3.2018/formatter/citation/common.xsl`.
+
+An additional text may be stored in an online resource description with protocol `WWW:LINK-1.0-http--publication-URL`.
+
+![](img/citation-with-addition.png)
+
+Example: <https://doi.org/10.12770/ad07a55f-5de7-4abc-ba89-8899b16c4b59>
+
+## Configuration
+
+The citation can be displayed or not in the record view. Check the user interface configuration to customize it:
+
+![](img/citation-ui-config.png)
+
+## Format
+
+Citation can be provided in various formats:
+
+-   HTML
+-   Plain text
+-   RIS
+-   BibTex
+
+## API
+
+The citation can be displayed in the default XSL formatter used for the full view using: <http://localhost:8080/geonetwork/srv/api/records/a46af25c-f949-48a2-9b7e-ac472230cda8?language=all&citation=true>
+
+The formatter producing the citation can be accessed directly using: <http://localhost:8080/geonetwork/srv/api/records/31255efc-c5c1-7787-2ae6-b8fc4bcd6e55/formatters/citation?format=ris>
+
+To list available formats use: <http://localhost:8080/geonetwork/srv/api/records/31255efc-c5c1-7787-2ae6-b8fc4bcd6e55/formatters/citation?format=>?

docs/manual/docs/user-guide/associating-resources/doi.md

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+# Digital Object Identifier (DOI) {#doi}
+
+## Configuration
+
+The catalogue support DOI creation using:
+
+-   [DataCite API](https://support.datacite.org/docs/mds-api-guide).
+-   EU publication office API <https://ra.publications.europa.eu/servlet/ws/doidata?api=medra.org>
+
+Configure the API access point in the `admin console > settings`:
+
+![](img/doi-admin-console.png)
+
+A record can be downloaded using the DataCite format from the API using: <http://localhost:8080/geonetwork/srv/api/records/da165110-88fd-11da-a88f-000d939bc5d8/formatters/datacite?output=xml>
+
+## Creating the DOI
+
+Once configured, DOI can be created using the interface. DOI is created on demand. It means that a user must ask for creation of a DOI. When created, the task is notified by email to the reviewer of the group (by default, can be configured for administrator only using the notification level of the task).
+
+![](img/doi-request-menu.png)
+
+The task is assigned to a specific user. An optional due date and comment can be defined:
+
+![](img/doi-request-popup.png)
+
+After submission of the task, the task owner is notified by email (if the mail server is configured, see admin console > settings). The task can then be resolved in the admin console > information > versioning section.
+
+If the configuration is missing or wrong, the error is reported:
+
+![](img/doi-config-wrong.png)
+
+For DOI creation, the task is a 2 steps actions:
+
+> -   First check if all prerequisite are covered (below the record is not valid in DataCite format).
+
+The DataCite format requires some mandatory fields:
+
+> -   Identifier (with mandatory type sub-property)
+> -   Creator (with optional given name, family name, name identifier and affiliation sub-properties)
+> -   Title (with optional type sub-properties)
+> -   Publisher
+> -   PublicationYear
+> -   ResourceType (with mandatory general type description subproperty)
+
+The mapping with ISO standards is the following:
+
+  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  Property          ISO 19139                                                                                                   ISO 19115-3
+  ----------------- ----------------------------------------------------------------------------------------------------------- -----------------------------------------------------------------------------------------------------------
+  Identifier        gmd:MD_Metadata/gmd:fileIdentifier/*/text()                                                                mdb:MD_Metadata/mdb:metadataIdentifier/*/mcc:code/*/text()
+
+  Creator           gmd:identificationInfo/*/gmd:pointOfContact with role 'pointOfContact' or 'custodian'                  mdb:identificationInfo/*/mri:pointOfContact with role 'pointOfContact' or 'custodian'
+
+  Title             gmd:identificationInfo/*/gmd:citation/*/gmd:title                                                         mdb:identificationInfo/*/mri:citation/*/cit:title
+
+  Publisher         gmd:distributorContact[1]/*/gmd:organisationName/gco:CharacterString                                     mrd:distributorContact[1]/*/cit:party/*/cit:organisationName/gco:CharacterString
+
+  PublicationYear   gmd:identificationInfo/*/gmd:citation/*/gmd:date/*[gmd:dateType/*/@codeListValue = 'publication']   mdb:identificationInfo/*/mri:citation/*/cit:date/*[cit:dateType/*/@codeListValue = 'publication']
+
+  ResourceType      gmd:hierarchyLevel/*/@codeListValue                                                                        mdb:metadataScope/*/mdb:resourceScope/*/@codeListValue
+  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+The mapping can be customized in:
+
+-   ISO19139 `schemas/iso19139/src/main/plugin/iso19139/formatter/datacite/view.xsl`
+-   ISO19115-3.2018 `schemas/iso19139/src/main/plugin/iso19139/formatter/datacite/view.xsl`
+
+See <http://schema.datacite.org/meta/kernel-4.1/doc/DataCite-MetadataKernel_v4.1.pdf> for more details on the format.
+
+DataCite API return XSD validation error.
+
+![](img/doi-request-check.png)
+
+The catalogue also allow to apply DataCite validation in the editor:
+
+![](img/doi-validation.png)
+
+A DOI may already be assigned for a record:
+
+![](img/doi-exists.png)
+
+In such case the DOI can be updated. If the DOI is already assigned in a metadata record, editors can also update the DOI from the editor:
+
+![](img/doi-update-in-editor.png)
+
+After validation, create the DOI
+
+![](img/doi-request-check-ok.png)
+
+Once created, a link to the DOI and to the DataCite document is available:
+
+![](img/doi-created.png)
+
+The DOI is then added to the metadata record:
+
+![](img/doi-in-xml.png)
+
+## DOI API
+
+The REST API allows to access the DOI related operations:
+
+![](img/doi-api.png)
+
+The check preconditions API returns exception if one of the pre requisite is not met:
+
+> -   DataCite API is not configured
+> -   Record is not public
+> -   Record already has a DOI
+> -   Record is not valid for DataCite (ie. XSD errors returned by DataCite XSD validation)
+
+![](img/doi-api-check.png)
+
+When a DOI is created, the response return the following details:
+
+![](img/doi-api-done.png)
+
+The DOI is added to the metadata record using the following encoding:
+
+![](img/doi-in-xml.png)
+
+## Examples
+
+-   [Comment créer un DOI à partir de l'outil de catalogage Geonetwork, Annick Battais](https://sist19.sciencesconf.org/data/pages/SIST19_A_BATTAIS.pdf)

docs/manual/docs/user-guide/associating-resources/index.md

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+# Associating resources {#associating_resources}
+
+You can associate a record with different types of resources using the **Associated resources** panel. This topic describes how to associate resources.
+
+-   To add or edit associated resources, open the editor, and click Associate Resources to view the wizard panel.
+
+![](img/onlinesrc.png)
+
+Use the wizard panel to create or delete associated resources. A list of currently attached resources grouped by types is also provided.
+
+-   To add a new online resource, click on the top + caret.
+
+![](img/addresources.png)
+
+You can associate different types of resources:
+
+-   [Linking Documents](linking-documents.md)
+-   [Linking Records](linking-records.md)
+-   [Doi](doi.md)
+-   [Cite](cite.md)

docs/manual/docs/user-guide/associating-resources/linking-dataset-or-service.md

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+# Linking a dataset with a service {#linking-dataset-or-service}
+
+Metadata on dataset can be associated to metadata on services.
+
+!!! info "Todo"
+
+    Add more details on how/why/encoding
+
+
+``` xml
+<srv:operatesOn uuidref="b795de68-726c-4bdf-a62a-a42686aa5b6f"
+                      xlink:href="http://metawal.wallonie.be/geonetwork/srv/fre/csw?service=CSW&amp;request=GetRecordById&amp;version=2.0.2&amp;outputSchema=http://www.isotc211.org/2005/gmd&amp;elementSetName=full&amp;id=b795de68-726c-4bdf-a62a-a42686aa5b6f"/>
+```
+
+In a service metadata record, click the `Link to a dataset` button to open the record selector which list all datasets in the catalog. Optionally, the layer name may be define manually or from the list of the layers retrieved from the service (using the GetCapabilities).
+
+![](img/dataset.png)
+
+In a dataset metadata record, click the `Link to a service` button to open the record selector which list all services in the catalog.
+
+![](img/service.png)
+
+When confirming the association, both records will be affected by the change (depending on user privileges - ie. current user may not be allowed to modify the target record).

docs/manual/docs/user-guide/associating-resources/linking-documents.md

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+# Associating documents {#associating_resources_doc}
+
+You can associate a record with documents using a URL.
+
+A document could be an overview, a quality report, a website available in different formats (eg. png, jpg, pdf, html) on the web.
+
+-   [Using Filestore](using-filestore.md)
+-   [Linking Thumbnail](linking-thumbnail.md)
+-   [Linking Online Resources](linking-online-resources.md)

docs/manual/docs/user-guide/associating-resources/linking-feature-catalog.md

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+# Describing attributes table in a feature Catalog {#linking-feature-catalog}
+
+A feature catalog describes the data model of the dataset with the list of tables, attributes, definitions, list of values, \... Feature catalogs could be described:
+
+-   as a document (eg. PDF) and linked to the metadata record (see [linking-online-resources-doc](linking-online-resources-doc.md))
+-   as a record and described using the ISO19110 standards.
+
+Click on `Link to a feature catalog` to open the record selector listing all feature catalog described in the catalog. Choose one and submit to associate the 2 documents.
+
+![](img/feature.png)
+
+In ISO19115-3, the feature catalog can also be described directly in the metadata record in the `content` section.
+
+!!! info "Todo"
+
+    Add encoding
+